I would not be surprised if Mewtwo doesn't come back. Melee has Pikachu, Jiggly, Mewtwo and Pichu all which promoted Gen 1 and 2 of pokemon, with Crystal having been released shortly before Melee. Lucario replaced Mewtwo as Gen 4 has just came out and they wanted to promote Diamond and Pearl while Poke Trainer replaced Pichu probably because of FireRed and Leafgreen and possibly the anime. As for Smash 4, Greninja promotes X and Y along with the vets Pikachu and Jiggly. As for why they kept Lucario...no idea. Maybe Lucario was just a popular enough character that they wanted to keep him. Given the popularity of Mewtwo, they *could* bring him back since he's a legendary in X and Y but theres always a chance he wont. I'm also hoping that Mewtwo doesn't return for another reason: Over-representation. Pokemon will have 4 reps already, and while 4 is a fine number to have, there are other series that only have one or two. Like Metroid. and while I know that Mewtwo's inclusion won't exclusively make Ridley, Kraid, Rundas or Dark Samus not be in the game, it would be a huge middle finger to have all these new and returning characters for other series and then just have Samus crying alone because her only friends are dead
TL;DR Theres hope for him, but don't really count on him returning.